[chimerax-users] display options for model with 2 chains

[Elaine Meng]

Hi Mauricio,
Probably the "real" way to do it is to save two images, one of each chain with the other one hidden, and then use a separate image-editing app like Gimp or Photoshop to composite the two images together.  I wonder if that is what the I-tasser folks did.

The only other idea I had seemed like cheating, to actually Z-translate the purple model closer to the user.  Also it might not look right, even if you change from perspective projection to orthoscopic (command "camera ortho")

I am not a programmer so I would not be the one to figure out an algorithm or how feasible it would be to implement, i.e. I'll create a feature request ticket and put you on the notification list, but can't say anything about how it will be prioritized.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Apr 1, 2022, at 8:17 AM, Mauricio Losilla via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> I am sorry, I didn't explain myself well, I will try to do it here. I was able to use all your tips successfully: I split the chain in two models, and tweaked the thickness, width, and transparency at will. It worked great! I am attaching the result. I think it accomplishes my original goal fairly well: to visually represent the fit of the gray protein to the purple template. 
> 
> However, the purple chain still looks sewed into the gray chain. In the image, this is better seen in the horizontal beta sheets at the center. The ideal display I was after is that of the image with the rainbow-colored chain and the purple template I sent in my original email. There, the purple chain always looks "on top" of the rainbow chain. That is what I meant yesterday with "the ability to superimpose the view of one chain". 
> 
> In case it is helpful, the reference image and the PDB file came from I-TASSER.
> 
> I am new to ChimeraX (and to 3D shapes of molecules in general), so I apologize if I am not making much sense. 
> 
> Thank you!
> 
> <result.png>
> 
> 
> Mauricio Losilla, PhD
> Integrative Biology; and Ecology, Evolution, & Behavior
> Michigan State University
> he, him, his
> 
> 
> On Thu, Mar 31, 2022 at 5:11 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Mauricio,
> I don't understand "the ability to superimpose the view of one chain" -- can you explain it in more words?  What is it that you want, that cannot be done currently?  Maybe it is already possible but I didn't explain it because I didn't realize that was what you wanted.
> 
> If you mean to make "cartoon style" work on just a chain instead of whole model, it may be unlikely since the settings it controls are per-model (not per-chain or per-residue).  However, it is already easy to split chains into separate models with "split."
> 
> Sorry if I am misunderstanding what you meant, however.
> Elaine  
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Mar 31, 2022, at 3:42 PM, Mauricio Losilla via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Hi Elaine,
> > 
> > Thank you very much for your prompt reply. Your workarounds were very helpful, I was able to tweak thickness and transparency, and arrived at a satisfactory display composition. Would you consider as a request feature the ability to superimpose the view of one chain?
> > 
> > Thank you!
> > Mau
> > 
> > Mauricio Losilla, PhD
> > Integrative Biology; and Ecology, Evolution, & Behavior
> > Michigan State University
> > he, him, his
> > 
> > 
> > On Thu, Mar 31, 2022 at 11:43 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Mauricio,
> > Some ideas are to:
> > 
> > - make the gray ribbon transparent
> > and/or
> > - make the purple one thicker
> > 
> > I can't tell from your question whether they are in two separate models or not.  Even if they're together in one PDB file they can be defined as separate models (as is done for NMR ensembles, e.g. PDB 1kfp).  If the purple one is model #1 and the gray one is #2, could be something like:
> > 
> > cartoon style #1 width 1 thick 1 xsect round
> > transparency #2 50 targ r
> > 
> > ...of course, you could use different width/thickness and transparency values.  
> > 
> > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html*style__;Iw!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XapFhvyuc$ >
> > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44Xa-fKcbds$ >
> > 
> > The cartoon style command works on whole models, so you would need them to be in separate models for that approach.  If your current PDB file does not have them in separate models, you could either text-edit it to add MODEL and ENDMDL records, or (probably easier) use the "split" command after opening it.
> > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XaI58NOwM$ >
> > 
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > 
> > > On Mar 31, 2022, at 10:02 AM, Mauricio Losilla via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > > 
> > > Hi,
> > > 
> > > I am new to ChimeraX, thank you for making this great software available.
> > > 
> > > I loaded a pdb file that has 2 amino acid chains aligned (chimerax.png). These chains are a model (gray) and template (purple). 
> > > 
> > > As you can see, the two chains look weaved or blended. I would much prefer to display the uninterrupted template around to model, to visually represent their fit. Is there a way to do this? 
> > > 
> > > I am attaching a second image (ideal_display.png, generated elsewhere) with the visual outcome I am after (the purple chain is the template, the rainbow-colored chain is the model). 
> > > 
> > > Thank you
> > > Mauricio Losilla, PhD
> > > Integrative Biology; and Ecology, Evolution, & Behavior
> > > Michigan State University
> > > he, him, his
> > > <ideal_display.png><chimerax.png>
> 
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